Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice
Rice foot rot disease caused by the pathogen Dickeya zeae (formerly known as Erwinia chrysanthemi pv. zeae), is a newly emerging damaging bacterial disease in China and the southeast of Asia, resulting in the loss of yield and grain quality. However, the genetic resistance mechanisms mediated by miR...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2019-01-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1422-0067/20/1/222 |
| _version_ | 1811239788237291520 |
|---|---|
| author | Wenqi Li Yulin Jia Fengquan Liu Fangquan Wang Fangjun Fan Jun Wang Jinyan Zhu Yang Xu Weigong Zhong Jie Yang |
| author_facet | Wenqi Li Yulin Jia Fengquan Liu Fangquan Wang Fangjun Fan Jun Wang Jinyan Zhu Yang Xu Weigong Zhong Jie Yang |
| author_sort | Wenqi Li |
| collection | DOAJ |
| description | Rice foot rot disease caused by the pathogen Dickeya zeae (formerly known as Erwinia chrysanthemi pv. zeae), is a newly emerging damaging bacterial disease in China and the southeast of Asia, resulting in the loss of yield and grain quality. However, the genetic resistance mechanisms mediated by miRNAs to D. zeae are unclear in rice. In the present study, 652 miRNAs including osa-miR396f predicted to be involved in multiple defense responses to D. zeae were identified with RNA sequencing. A total of 79 differentially expressed miRNAs were detected under the criterion of normalized reads ≥10, including 51 known and 28 novel miRNAs. Degradome sequencing identified 799 targets predicted to be cleaved by 168 identified miRNAs. Among them, 29 differentially expressed miRNA and target pairs including miRNA396f-OsGRFs were identified by co-expression analysis. Overexpression of the osa-miR396f precursor in a susceptible rice variety showed enhanced resistance to D. zeae, coupled with significant accumulation of transcripts of osa-miR396f and reduction of its target the Growth-Regulating Factors (OsGRFs). Taken together, these findings suggest that miRNA and targets including miR396f-OsGRFs have a role in resisting the infections by bacteria D. zeae. |
| first_indexed | 2024-04-12T13:07:19Z |
| format | Article |
| id | doaj.art-8cd83b01300d44ab8626d930d37bf75a |
| institution | Directory Open Access Journal |
| issn | 1422-0067 |
| language | English |
| last_indexed | 2024-04-12T13:07:19Z |
| publishDate | 2019-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-8cd83b01300d44ab8626d930d37bf75a2022-12-22T03:32:00ZengMDPI AGInternational Journal of Molecular Sciences1422-00672019-01-0120122210.3390/ijms20010222ijms20010222Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant RiceWenqi Li0Yulin Jia1Fengquan Liu2Fangquan Wang3Fangjun Fan4Jun Wang5Jinyan Zhu6Yang Xu7Weigong Zhong8Jie Yang9Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, ChinaUnited States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USAInstitute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, ChinaInstitute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, ChinaInstitute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, ChinaInstitute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, ChinaInstitute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, ChinaInstitute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, ChinaInstitute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, ChinaInstitute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing 210014, ChinaRice foot rot disease caused by the pathogen Dickeya zeae (formerly known as Erwinia chrysanthemi pv. zeae), is a newly emerging damaging bacterial disease in China and the southeast of Asia, resulting in the loss of yield and grain quality. However, the genetic resistance mechanisms mediated by miRNAs to D. zeae are unclear in rice. In the present study, 652 miRNAs including osa-miR396f predicted to be involved in multiple defense responses to D. zeae were identified with RNA sequencing. A total of 79 differentially expressed miRNAs were detected under the criterion of normalized reads ≥10, including 51 known and 28 novel miRNAs. Degradome sequencing identified 799 targets predicted to be cleaved by 168 identified miRNAs. Among them, 29 differentially expressed miRNA and target pairs including miRNA396f-OsGRFs were identified by co-expression analysis. Overexpression of the osa-miR396f precursor in a susceptible rice variety showed enhanced resistance to D. zeae, coupled with significant accumulation of transcripts of osa-miR396f and reduction of its target the Growth-Regulating Factors (OsGRFs). Taken together, these findings suggest that miRNA and targets including miR396f-OsGRFs have a role in resisting the infections by bacteria D. zeae.http://www.mdpi.com/1422-0067/20/1/222rice foot rot diseaseDickeya zeaemicroRNARNA and degradome sequencingdisease resistance |
| spellingShingle | Wenqi Li Yulin Jia Fengquan Liu Fangquan Wang Fangjun Fan Jun Wang Jinyan Zhu Yang Xu Weigong Zhong Jie Yang Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice International Journal of Molecular Sciences rice foot rot disease Dickeya zeae microRNA RNA and degradome sequencing disease resistance |
| title | Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice |
| title_full | Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice |
| title_fullStr | Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice |
| title_full_unstemmed | Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice |
| title_short | Integration Analysis of Small RNA and Degradome Sequencing Reveals MicroRNAs Responsive to Dickeya zeae in Resistant Rice |
| title_sort | integration analysis of small rna and degradome sequencing reveals micrornas responsive to dickeya zeae in resistant rice |
| topic | rice foot rot disease Dickeya zeae microRNA RNA and degradome sequencing disease resistance |
| url | http://www.mdpi.com/1422-0067/20/1/222 |
| work_keys_str_mv | AT wenqili integrationanalysisofsmallrnaanddegradomesequencingrevealsmicrornasresponsivetodickeyazeaeinresistantrice AT yulinjia integrationanalysisofsmallrnaanddegradomesequencingrevealsmicrornasresponsivetodickeyazeaeinresistantrice AT fengquanliu integrationanalysisofsmallrnaanddegradomesequencingrevealsmicrornasresponsivetodickeyazeaeinresistantrice AT fangquanwang integrationanalysisofsmallrnaanddegradomesequencingrevealsmicrornasresponsivetodickeyazeaeinresistantrice AT fangjunfan integrationanalysisofsmallrnaanddegradomesequencingrevealsmicrornasresponsivetodickeyazeaeinresistantrice AT junwang integrationanalysisofsmallrnaanddegradomesequencingrevealsmicrornasresponsivetodickeyazeaeinresistantrice AT jinyanzhu integrationanalysisofsmallrnaanddegradomesequencingrevealsmicrornasresponsivetodickeyazeaeinresistantrice AT yangxu integrationanalysisofsmallrnaanddegradomesequencingrevealsmicrornasresponsivetodickeyazeaeinresistantrice AT weigongzhong integrationanalysisofsmallrnaanddegradomesequencingrevealsmicrornasresponsivetodickeyazeaeinresistantrice AT jieyang integrationanalysisofsmallrnaanddegradomesequencingrevealsmicrornasresponsivetodickeyazeaeinresistantrice |